Resignation while on unauthorised absence previously requested for Study leave

I am an emoloyee of central govt. PSU. I requested permission from my organziation for 24 months extraordinary leave for study purpose. It was duly forwarded by my competent authority, HoD but it did not get sanctioned from Head HR. I sent multiple reminders all in vain. Initially, I was sick so left my station on medical ground. Since there was too much delay from organization, I proceeded with my studies. Everytime I mentioned "Leave without pay" still management credited salary to my account for 9 months since I left station. One fine day, they send me "unauthorised absence" notice. I replied. Such notice came two times more, I replied to each plus again sent reminder to HR for considering my absence as EOL for study prupose. Now, I want to resign from the service outright due to personal and family reasons. Even my family reasons are very well known to my organization. I want to resign with immediate effect. They are telling, if I join, they will hold disciplinary action, which will take a lot of time like typical govt. Organization. One suggestion came of resigning while still on the so called "absence". My query is will I be called for disciplinary action if I resign with immediate effect. ? I am totally okay with paying the financial obligations which the authorities paid due to their lack of promptness. If I am okay with paying dues, and if they want they can also reduce my work experience by my period of absence.